11e45667d4e291b3038ccda729a1cdf5bcaf004a braney Mon Jul 11 15:46:54 2016 -0700 incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX defines, modify a bunch of makefiles to include kentSrc variable pointing to top of the tree. diff --git src/htslib/test/fieldarith.sam src/htslib/test/fieldarith.sam new file mode 100644 index 0000000..180d1e8 --- /dev/null +++ src/htslib/test/fieldarith.sam @@ -0,0 +1,15 @@ +@SQ SN:one LN:1000 +@SQ SN:two LN:500 +@CO For each SAM record that has each listed aux field, performs these tests: +@CO XQ is the expected result for bam_cigar2qlen() +@CO XR is the expected result for bam_cigar2rlen() +@CO XE is the expected result for bam_endpos() +@CO (Note that these are all zero-based, while POS is one-based in SAM) +r1 0 one 50 20 8M * 0 0 ATGCATGC qqqqqqqq XQ:i:8 XR:i:8 XE:i:57 +r2 0 one 100 20 50M * 0 0 ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq XQ:i:50 XR:i:50 XE:i:149 +unmapped 5 two 200 0 * two 200 0 ATGCATGC qqqqqqqq XQ:i:0 XR:i:0 XE:i:200 +hascigar 5 two 200 0 6M2S two 200 0 ATGCATGC qqqqqqqq XQ:i:8 XR:i:6 XE:i:200 +s1 0 one 300 20 2M * 0 0 AT qq XQ:i:2 XR:i:2 XE:i:301 +su1 4 * 0 0 * * 0 0 AT qq XQ:i:0 XR:i:0 XE:i:0 +su2 5 two 400 0 * two 400 0 AT qq XQ:i:0 XR:i:0 XE:i:400 +su3 4 one 500 0 2M * 0 0 AT qq XQ:i:2 XR:i:2 XE:i:500